Some Isomers of Nevirapine - A DFT Study
Abstract
Nevirapine is a dipyridodiazepinone and representative of a new class of anti-HIV agents, the non-nucleoside reverse transcriptase inhibitors. The effect of some centric perturbations on some properties of nevirapine have been investigated within the limitations of density at the level of B3LYP/6-31++G(d,p). The calculations have revealed that the isomers constructed are all thermally favorable and electronically stable. Various calculated properties of the isomers including geometrical, electronic, thermo chemical, quantum chemical and some spectral properties have been harvested and discussed. Additionally, nucleus-independent chemical shift, NICS(0), calculations have been performed and the effect of perturbations on the local aromaticity of six-membered rings have been investigated. The effect of monocentric carbon to nitrogen perturbations on the chemical function descriptors have been determined. Also, the variation of polar surface areas (PSA) of the isomers have been considered in relation to their ability to penetrate the blood-brain barrier.
References
Grozinger, K., Proudfoot, J., & Hargrave, K. (2006). Discovery and development of nevirapine. In M.S. Chorghade (Ed.). Drug discovery and development: Drug discovery (V. 1, Ch.13, pp. 353-363). NY: Wiley. https://doi.org/10.1002/0471780103.ch13
Patel, S.S., & Benfield, P. (1996). Nevirapine. Clin. lmmunother., 6(4), 307-317. https://doi.org/10.1007/BF03259093
Milinkovic, A., & Martinez, E. (2004). Nevirapine in the treatment of AIDS, Experts. Rev. Anri-infect. Ther., 2(3), 367-373. https://doi.org/10.1586/14787210.2.3.367
Spence, R.A., Kati, W.M., Anderson, K.S., & Johnson, K.A. (1995). Mechanism of inhibition of HIV-I reverse transcriptase by nonnucleoside inhibitors. Science, 267, 988-93. https://doi.org/10.1126/science.7532321
Palaniappan, C., Fay, P.J., & Bambara, R.A. (1995). Nevirapine alters the cleavage specificity of ribonuclease H of human immunodeficiency virus I reverse transcriptase. J. Bioi. Chern., 270(9), 4861-9. https://doi.org/10.1074/jbc.270.9.4861
Mui, P.W., Jacober, S.P., Hargrave, K.D., & Adams, J. (1992). Crystal structure of nevirapine, a non-nucleoside inhibitor of HIV-1 reverse transcriptase, and computational alignment with a structurally diverse inhibitor. Journal of Medicinal Chemistry, 35(1), 201-202. https://doi.org/10.1021/jm00079a029
Caira, M.R., Stieger, N., Liebenberg, W., De Villiers, M.M., & Samsodien, H. (2008). Solvent inclusion by the anti-HIV drug nevirapine: X-ray structures and thermal decomposition of representative solvates. Crystal Growth & Design, 8(1), 17-23. https://doi.org/10.1021/cg070522r
Burke, E.W.D., Morris, G.A., Vincent, M.A., Hillier, I.H., & Clayden, J. (2012). Is nevirapine atropisomeric? Experimental and computational evidence for rapid conformational inversion. Org. Biomol. Chem., 10, 716-719. https://doi.org/10.1039/C1OB06490H
Diab, S., McQuade, D.T., Gupton, B.F., & Gerogiorgis, D.I. (2019). Process design and optimization for the continuous manufacturing of nevirapine, an active pharmaceutical ingredient for HIV treatment. Organic Process Research & Development, 23(3), 320-333. https://doi.org/10.1021/acs.oprd.8b00381
Sylvain, B., Defoy, D., Dory, Y.L., & Klarskov, K. (2009). Efficient synthesis of nevirapine analogs to study its metabolic profile by click fishing. Bioorganic & Medicinal Chemistry Letters, 19(21), 6127-6130. https://doi.org/10.1016/j.bmcl.2009.09.011
Sharma, A.M., Klarskov, K., & Uetrecht, J. (2013). Nevirapine bioactivation and covalent binding in the skin. Chemical Research in Toxicology, 26(3), 410-421. https://doi.org/10.1021/tx3004938
Bhat, J.I., & Alva, V.D.P. (2011). Inhibition effect of nevirapine an antiretroviral on the corrosion of mild steel under acidic condition. Journal of the Korean Chemical Society, 55(5), 835-841. https://doi.org/10.5012/JKCS.2011.55.5.835
Bhembe, Y.A., Lukhele, L.P., Hlekelele, L., Ray, S.S., Sharma, A., Vo, D-V.N., & Dlamini, L.N. (2020). Photocatalytic degradation of nevirapine with a heterostructure of few-layer black phosphorus coupled with niobium (V) oxide nanoflowers (FL BP@Nb2O5). Chemosphere, 261, 128159. https://doi.org/10.1016/j.chemosphere.2020.128159
Apath, D., Moyo, M., & Shumba, M. (2020). TiO2 nanoparticles decorated graphene nanoribbons for voltammetric determination of an anti-HIV drug nevirapine. Journal of Chemistry, 2020, Article ID 3932715, 13 pp. https://doi.org/10.1155/2020/3932715
Tateishi, Y., Ohe, T., Yasuda, D., Takahashi, K., Nakamura, S., Kazuki, Y., & Mashino, T. (2020). Synthesis and evaluation of nevirapine analogs to study the metabolic activation of nevirapine. Drug Metabolism and Pharmacokinetics, 35(2), 238-243, https://doi.org/10.1016/j.dmpk.2020.01.006
Sathisaran, I., & Dalvi, S.V. (2021). Cocrystallization of an antiretroviral drug nevirapine: an eutectic, a cocrystal solvate, and a cocrystal hydrate. Crystal Growth & Design, 21(4), 2076-2092. https://doi.org/10.1021/acs.cgd.0c01513
Ayala, A.P., Siesler, H.W., Wardell, S.M.S.V., Boechat, N., Dabbene, V., & Cuffni, S.L. (2007). Vibrational spectra and quantum mechanical calculations of antiretroviral drugs: Nevirapine. J. Mol. Struct., 828(1-3), 201-210. https://doi.org/10.1016/j.molstruc.2006.05.055
Vailikhit, V., Bunsawansong, P., Techasakul, S., & Hannongbua, S. (2006). Conformational analysis of nevirapine in solutions based on nmr spectroscopy and quantum chemical calculations. J. Theor. Comput. Chem., 5(4), 913-924. https://doi.org/10.1142/S0219633606002702
Parreira, R.L.T., Abrahão-Júnior, O., & Galembeck, S.E. (2001). Conformational preferences of non-nucleoside HIV-1 reverse transcriptase inhibitors. Tetrahedron, 57(16), 3243-3253. https://doi.org/10.1016/S0040-4020(01)00193-4
Abrahão-Júnior, O., Nascimento, P.G.B.D., & Galembeck, S.E. (2001). Conformational analysis of the HIV-1 virus reverse transcriptase nonnucleoside inhibitors: TIBO and nevirapine. J. Comput.Chem., 22(15), 1817-1829. https://doi.org/10.1002/jcc.1133
Hannongbua, S., Prasithichokekul, S., & Pungpo, P.(2001). Conformational analysis of nevirapine, a non-nucleoside HIV-1 reverse transcriptase inhibitor, based on quantum mechanical calculations. J. Comput. Aided Mol. Des., 15, 997-1004. https://doi.org/10.1023/A:1014881723431
Stewart, J.J.P. (1989). Optimization of parameters for semi empirical methods I. J. Comput. Chem., 10, 209-220. https://doi.org/10.1002/jcc.540100208
Stewart, J.J.P. (1989). Optimization of parameters for semi empirical methods II. J. Comput. Chem., 10, 221-264. https://doi.org/10.1002/jcc.540100209
Leach, A.R. (1997). Molecular modeling. Essex: Longman.
Kohn, W., & Sham, L.J. (1965). Self-consistent equations including exchange and correlation effects. Phys. Rev., 140, 1133-1138. https://doi.org/10.1103/PhysRev.140.A1133
Parr, R.G., & Yang, W. (1989). Density functional theory of atoms and molecules. London: Oxford University Press.
Becke, A.D. (1988). Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A, 38, 3098-3100. https://doi.org/10.1103/PhysRevA.38.3098
Vosko, S.H., Wilk, L., & Nusair, M. (1980). Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis. Can. J. Phys., 58, 1200-1211. https://doi.org/10.1139/p80-159
Lee, C., Yang, W., & Parr, R.G. (1988). Development of the Colle-Salvetti correlation energy formula into a functional of the electron density. Phys. Rev. B, 37, 785-789. https://doi.org/10.1103/PhysRevB.37.785
SPARTAN 06 (2006). Wavefunction Inc. Irvine CA, USA.
Gaussian 03, Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Montgomery, Jr., J.A., Vreven, T., Kudin, K.N., Burant, J.C., Millam, J.M., Iyengar, S.S., Tomasi, J., Barone, V., Mennucci, B., Cossi, M., Scalmani, G., Rega, N., Petersson, G.A., Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Klene, M., Li, X., Knox, J.E., Hratchian, H.P., Cross, J.B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R.E., Yazyev, O., Austin, A.J., Cammi, R., Pomelli, C., Ochterski, J.W., Ayala, P.Y., Morokuma, K., Voth, G.A., Salvador, P., Dannenberg, J.J., Zakrzewski, V.G., Dapprich, S., Daniels, A.D., Strain, M.C., Farkas, O., Malick, D.K., Rabuck, A.D., Raghavachari, K., Foresman, J.B., Ortiz, J.V., Cui, Q., Baboul, A.G., Clifford, S., Cioslowski, J., Stefanov, B.B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Martin, R.L., Fox, D.J., Keith, T., Al-Laham, M.A., Peng, C.Y. Nanayakkara, A., Challacombe, M., Gill, P.M.W., Johnson, B., Chen, W., Wong, M.W., Gonzalez, C., & Pople, J.A., Gaussian, Inc., Wallingford CT, 2004.
Mui, P.W., Jacober, S.P., Hargrave, K.D., & Adams, J. (1992). Crystal structure of nevirapine, a non-nucleoside inhibitor of HIV-1 reverse transcriptase, and computational alignment with a structurally diverse inhibitor. Journal of Medicinal Chemistry, 35(1), 201-202. https://doi.org/10.1021/jm00079a029
Reichardt, C. (2004). Solvent effects and solvent effects in organic chemistry. Weinheim: Wiley-VCH.
Hitchcock, S.A., & Pennington, L.D. (2006). Structure-brain exposure relationships. J. Med. Chem., 49(26), 7559-7583. https://doi.org/10.1021/jm060642i. PMID 17181137.
Shityakov, S., Neuhaus, W., Dandekar, T., & Förster, C. (2013). Analysing molecular polar surface descriptors to predict blood-brain barrier permeation. International Journal of Computational Biology and Drug Design, 6(1-2), 146-56. https://doi.org/10.1504/IJCBDD.2013.052195. PMID 23428480.
Minkin, V.I., Glukhovtsev, M.N., & Simkin, B.Y. (1994). Aromaticity and antiaromaticity: Electronic and structural aspects. New York: Wiley.
Schleyer, P.R., & Jiao, H. (1996). What is aromaticity?. Pure Appl. Chem., 68, 209-218. https://doi.org/10.1351/pac199668020209
Glukhovtsev, M.N. (1997). Aromaticity today: energetic and structural criteria. J. Chem. Educ., 74, 132-136. https://doi.org/10.1021/ed074p132
Krygowski, T.M., Cyranski, M.K., Czarnocki, Z., Hafelinger, G., & Katritzky, A.R. (2000). Aromaticity: a theoretical concept of immense practical importance. Tetrahedron, 56, 1783-1796. https://doi.org/10.1016/s0040-4020(99)00979-5
Schleyer, P.R. (2001). Introduction: aromaticity. Chem. Rev., 101, 1115-1118. https://doi.org/10.1021/cr0103221
Cyranski, M.K., Krygowski, T.M., Katritzky, A.R., & Schleyer, P.R. (2002). To what extent can aromaticity be defined uniquely?. J. Org. Chem., 67, 1333-1338. https://doi.org/10.1021/jo016255s
Chen, Z., Wannere, C.S., Corminboeuf, C., Puchta, R., & Schleyer, P. von R. (2005). Nucleus independent chemical shifts (NICS) as an aromaticity criterion. Chem. Rev., 105(10), 3842-3888. https://doi.org/10.1021/cr030088
Gershoni-Poranne, R., & Stanger, A. (2015). Magnetic criteria of aromaticity. Chem. Soc.Rev., 44(18), 6597-6615. https://doi.org/10.1039/c5cs00114e
Dickens, T.K., & Mallion, R.B. (2016). Topological ring-currents in conjugated systems. MATCH Commun. Math. Comput. Chem., 76, 297-356.
Stanger, A. (2010). Obtaining relative induced ring currents quantitatively from NICS. J. Org. Chem., 75(7), 2281-2288. https://doi.org/10.1021/jo1000753
Monajjemi, M., & Mohammadian, N.T. (2015). S-NICS: An aromaticity criterion for nano molecules. J. Comput. Theor. Nanosci., 12(11), 4895-4914. https://doi.org/10.1166/jctn.2015.4458
Schleyer, P.R., Maerker, C., Dransfeld, A., Jiao, H., & Hommes, N.J.R.E. (1996). Nucleus independent chemical shifts: a simple and efficient aromaticity probe. J. Am. Chem. Soc., 118(26), 6317-6318. https://doi.org/10.1021/ja960582d. PMID: 28872872.
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